JAL-2008 avoid unnecessary repaints; signatures changed from String[] to

List<String>

diff --git a/src/jalview/analysis/scoremodels/FeatureScoreModel.java b/src/jalview/analysis/scoremodels/FeatureScoreModel.java
index 69538d5..1ca3342 100644 (file)
--- a/src/jalview/analysis/scoremodels/FeatureScoreModel.java
+++ b/src/jalview/analysis/scoremodels/FeatureScoreModel.java
@@ -28,7 +28,6 @@ import jalview.datamodel.SequenceI;
 import jalview.util.Comparison;
 
 import java.util.ArrayList;
-import java.util.Arrays;
 import java.util.Hashtable;
 import java.util.List;
 
@@ -48,12 +47,9 @@ public class FeatureScoreModel implements ScoreModelI, ViewBasedAnalysisI
   public float[][] findDistances(AlignmentView seqData)
   {
     int nofeats = 0;
-    List<String> dft = Arrays.asList(fr.getDisplayedFeatureTypes());
+    List<String> dft = fr.getDisplayedFeatureTypes();
 
-    if (dft != null)
-    {
-      nofeats = dft.size();
-    }
+    nofeats = dft.size();
 
     SequenceI[] sequenceString = seqData.getVisibleAlignment(
             Comparison.GapChars.charAt(0)).getSequencesArray();
@@ -151,6 +147,7 @@ public class FeatureScoreModel implements ScoreModelI, ViewBasedAnalysisI
     return true;
   }
 
+  @Override
   public String toString()
   {
     return "Score between sequences based on hamming distance between binary vectors marking features displayed at each column";

diff --git a/src/jalview/api/AlignViewControllerI.java b/src/jalview/api/AlignViewControllerI.java
index a2f2204..17a1563 100644 (file)
--- a/src/jalview/api/AlignViewControllerI.java
+++ b/src/jalview/api/AlignViewControllerI.java
@@ -20,6 +20,8 @@
  */
 package jalview.api;
 
+import java.util.List;
+
 /**
  * prototype abstract controller for a Jalview alignment view
  * 
@@ -71,7 +73,7 @@ public interface AlignViewControllerI
    * @param typ
    *          list of feature names or null to use currently displayed features
    */
-  void sortAlignmentByFeatureScore(String[] typ);
+  void sortAlignmentByFeatureScore(List<String> typ);
 
   /**
    * sort the alignment or current selection by distribution of the given set of
@@ -80,7 +82,7 @@ public interface AlignViewControllerI
    * @param typ
    *          list of feature names or null to use currently displayed features
    */
-  void sortAlignmentByFeatureDensity(String[] typ);
+  void sortAlignmentByFeatureDensity(List<String> typ);
 
   /**
    * add a features file of some kind to the current view

diff --git a/src/jalview/api/FeatureRenderer.java b/src/jalview/api/FeatureRenderer.java
index 0d0adaa..5b15cad 100644 (file)
--- a/src/jalview/api/FeatureRenderer.java
+++ b/src/jalview/api/FeatureRenderer.java
@@ -149,19 +149,19 @@ public interface FeatureRenderer
   boolean isTransparencyAvailable();
 
   /**
-   * get current displayed types
+   * get current displayed types, in ordering of rendering (on top last)
    * 
-   * @return
+   * @return a (possibly empty) list of feature types
    */
 
-  String[] getDisplayedFeatureTypes();
+  List<String> getDisplayedFeatureTypes();
 
   /**
    * get current displayed groups
    * 
-   * @return
+   * @return a (possibly empty) list of feature groups
    */
-  String[] getDisplayedFeatureGroups();
+  List<String> getDisplayedFeatureGroups();
 
   /**
    * display all features of these types

diff --git a/src/jalview/appletgui/FeatureSettings.java b/src/jalview/appletgui/FeatureSettings.java
index 23ca5ae..584a69a 100755 (executable)
--- a/src/jalview/appletgui/FeatureSettings.java
+++ b/src/jalview/appletgui/FeatureSettings.java
@@ -57,6 +57,7 @@ import java.awt.event.MouseListener;
 import java.awt.event.MouseMotionListener;
 import java.awt.event.WindowAdapter;
 import java.awt.event.WindowEvent;
+import java.util.Arrays;
 import java.util.Enumeration;
 import java.util.Hashtable;
 import java.util.List;
@@ -217,8 +218,8 @@ public class FeatureSettings extends Panel implements ItemListener,
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        me.ap.alignFrame.avc
-                .sortAlignmentByFeatureScore(new String[] { type });
+        me.ap.alignFrame.avc.sortAlignmentByFeatureScore(Arrays
+                .asList(new String[] { type }));
       }
 
     });
@@ -230,8 +231,8 @@ public class FeatureSettings extends Panel implements ItemListener,
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        me.ap.alignFrame.avc
-                .sortAlignmentByFeatureDensity(new String[] { type });
+        me.ap.alignFrame.avc.sortAlignmentByFeatureDensity(Arrays
+                .asList(new String[] { type }));
       }
 
     });

diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java
index be84bbf..ca2ae6d 100644 (file)
--- a/src/jalview/controller/AlignViewController.java
+++ b/src/jalview/controller/AlignViewController.java
@@ -37,7 +37,6 @@ import jalview.io.FeaturesFile;
 import jalview.util.MessageManager;
 
 import java.awt.Color;
-import java.util.ArrayList;
 import java.util.BitSet;
 import java.util.List;
 
@@ -317,46 +316,23 @@ public class AlignViewController implements AlignViewControllerI
   }
 
   @Override
-  public void sortAlignmentByFeatureDensity(String[] typ)
+  public void sortAlignmentByFeatureDensity(List<String> typ)
   {
     sortBy(typ, "Sort by Density", AlignmentSorter.FEATURE_DENSITY);
   }
 
-  protected void sortBy(String[] typ, String methodText, final String method)
+  protected void sortBy(List<String> typ, String methodText,
+          final String method)
   {
     FeatureRenderer fr = alignPanel.getFeatureRenderer();
-    if (typ == null)
+    if (typ == null && fr != null)
     {
-      typ = fr == null ? null : fr.getDisplayedFeatureTypes();
+      typ = fr.getDisplayedFeatureTypes();
     }
-    String gps[] = null;
-    gps = fr == null ? null : fr.getDisplayedFeatureGroups();
-    if (typ != null)
+    List<String> gps = null;
+    if (fr != null)
     {
-      List<String> types = new ArrayList<String>();
-      for (String displayed : typ)
-      {
-        if (displayed != null)
-        {
-          types.add(displayed);
-        }
-      }
-      typ = new String[types.size()];
-      types.toArray(typ);
-    }
-    if (gps != null)
-    {
-      List<String> grps = new ArrayList<String>();
-
-      for (int i = 0; i < gps.length; i++)
-      {
-        if (gps[i] != null)
-        {
-          grps.add(gps[i]);
-        }
-      }
-      gps = new String[grps.size()];
-      grps.toArray(gps);
+      gps = fr.getDisplayedFeatureGroups();
     }
     AlignmentI al = viewport.getAlignment();
 
@@ -381,7 +357,7 @@ public class AlignViewController implements AlignViewControllerI
   }
 
   @Override
-  public void sortAlignmentByFeatureScore(String[] typ)
+  public void sortAlignmentByFeatureScore(List<String> typ)
   {
     sortBy(typ, "Sort by Feature Score", AlignmentSorter.FEATURE_SCORE);
   }

diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index 6b58b51..6ca0769 100644 (file)
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -54,6 +54,7 @@ import java.io.FileOutputStream;
 import java.io.InputStreamReader;
 import java.io.OutputStreamWriter;
 import java.io.PrintWriter;
+import java.util.Arrays;
 import java.util.Hashtable;
 import java.util.Iterator;
 import java.util.List;
@@ -164,6 +165,7 @@ public class FeatureSettings extends JPanel implements
 
     table.addMouseListener(new MouseAdapter()
     {
+      @Override
       public void mousePressed(MouseEvent evt)
       {
         selectedRow = table.rowAtPoint(evt.getPoint());
@@ -198,24 +200,19 @@ public class FeatureSettings extends JPanel implements
 
     table.addMouseMotionListener(new MouseMotionAdapter()
     {
+      @Override
       public void mouseDragged(MouseEvent evt)
       {
         int newRow = table.rowAtPoint(evt.getPoint());
         if (newRow != selectedRow && selectedRow != -1 && newRow != -1)
         {
-          Object[] temp = new Object[3];
-          temp[0] = table.getValueAt(selectedRow, 0);
-          temp[1] = table.getValueAt(selectedRow, 1);
-          temp[2] = table.getValueAt(selectedRow, 2);
-
-          table.setValueAt(table.getValueAt(newRow, 0), selectedRow, 0);
-          table.setValueAt(table.getValueAt(newRow, 1), selectedRow, 1);
-          table.setValueAt(table.getValueAt(newRow, 2), selectedRow, 2);
-
-          table.setValueAt(temp[0], newRow, 0);
-          table.setValueAt(temp[1], newRow, 1);
-          table.setValueAt(temp[2], newRow, 2);
-
+          Object[][] data = ((FeatureTableModel) table.getModel())
+                  .getData();
+          Object[] temp = data[selectedRow];
+          data[selectedRow] = data[newRow];
+          data[newRow] = temp;
+          updateFeatureRenderer(data);
+          table.repaint();
           selectedRow = newRow;
         }
       }
@@ -237,6 +234,7 @@ public class FeatureSettings extends JPanel implements
     final FeatureSettings fs = this;
     fr.addPropertyChangeListener(change = new PropertyChangeListener()
     {
+      @Override
       public void propertyChange(PropertyChangeEvent evt)
       {
         if (!fs.resettingTable && !fs.handlingUpdate)
@@ -267,6 +265,7 @@ public class FeatureSettings extends JPanel implements
 
     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
     {
+      @Override
       public void internalFrameClosed(
               javax.swing.event.InternalFrameEvent evt)
       {
@@ -289,9 +288,11 @@ public class FeatureSettings extends JPanel implements
     scr.addActionListener(new ActionListener()
     {
 
+      @Override
       public void actionPerformed(ActionEvent e)
       {
-        me.af.avc.sortAlignmentByFeatureScore(new String[] { type });
+        me.af.avc.sortAlignmentByFeatureScore(Arrays
+                .asList(new String[] { type }));
       }
 
     });
@@ -300,9 +301,11 @@ public class FeatureSettings extends JPanel implements
     dens.addActionListener(new ActionListener()
     {
 
+      @Override
       public void actionPerformed(ActionEvent e)
       {
-        me.af.avc.sortAlignmentByFeatureDensity(new String[] { type });
+        me.af.avc.sortAlignmentByFeatureDensity(Arrays
+                .asList(new String[] { type }));
       }
 
     });
@@ -337,6 +340,7 @@ public class FeatureSettings extends JPanel implements
         {
           JColorChooser colorChooser;
 
+          @Override
           public void actionPerformed(ActionEvent e)
           {
             if (e.getSource() == mxcol)
@@ -507,6 +511,7 @@ public class FeatureSettings extends JPanel implements
     check.setFont(new Font("Serif", Font.BOLD, 12));
     check.addItemListener(new ItemListener()
     {
+      @Override
       public void itemStateChanged(ItemEvent evt)
       {
         fr.setGroupVisibility(check.getText(), check.isSelected());
@@ -969,10 +974,19 @@ public class FeatureSettings extends JPanel implements
     updateFeatureRenderer(data, true);
   }
 
+  /**
+   * Update the priority order of features; only repaint if this changed the
+   * order of visible features
+   * 
+   * @param data
+   * @param visibleNew
+   */
   private void updateFeatureRenderer(Object[][] data, boolean visibleNew)
   {
-    fr.setFeaturePriority(data, visibleNew);
-    af.alignPanel.paintAlignment(true);
+    if (fr.setFeaturePriority(data, visibleNew))
+    {
+      af.alignPanel.paintAlignment(true);
+    }
   }
 
   int selectedRow = -1;
@@ -1029,6 +1043,7 @@ public class FeatureSettings extends JPanel implements
     invert.setText(MessageManager.getString("label.invert_selection"));
     invert.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         invertSelection();
@@ -1038,6 +1053,7 @@ public class FeatureSettings extends JPanel implements
     optimizeOrder.setText(MessageManager.getString("label.optimise_order"));
     optimizeOrder.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         orderByAvWidth();
@@ -1048,6 +1064,7 @@ public class FeatureSettings extends JPanel implements
             .setText(MessageManager.getString("label.seq_sort_by_score"));
     sortByScore.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         af.avc.sortAlignmentByFeatureScore(null);
@@ -1058,6 +1075,7 @@ public class FeatureSettings extends JPanel implements
             .getString("label.sequence_sort_by_density"));
     sortByDens.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         af.avc.sortAlignmentByFeatureDensity(null);
@@ -1067,6 +1085,7 @@ public class FeatureSettings extends JPanel implements
     help.setText(MessageManager.getString("action.help"));
     help.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         try
@@ -1082,6 +1101,7 @@ public class FeatureSettings extends JPanel implements
     help.setText(MessageManager.getString("action.help"));
     help.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         try
@@ -1097,6 +1117,7 @@ public class FeatureSettings extends JPanel implements
     cancel.setText(MessageManager.getString("action.cancel"));
     cancel.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         fr.setTransparency(originalTransparency);
@@ -1108,6 +1129,7 @@ public class FeatureSettings extends JPanel implements
     ok.setText(MessageManager.getString("action.ok"));
     ok.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         close();
@@ -1117,6 +1139,7 @@ public class FeatureSettings extends JPanel implements
     loadColours.setText(MessageManager.getString("label.load_colours"));
     loadColours.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         load();
@@ -1126,6 +1149,7 @@ public class FeatureSettings extends JPanel implements
     saveColours.setText(MessageManager.getString("label.save_colours"));
     saveColours.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         save();
@@ -1133,6 +1157,7 @@ public class FeatureSettings extends JPanel implements
     });
     transparency.addChangeListener(new ChangeListener()
     {
+      @Override
       public void stateChanged(ChangeEvent evt)
       {
         fr.setTransparency((100 - transparency.getValue()) / 100f);
@@ -1146,6 +1171,7 @@ public class FeatureSettings extends JPanel implements
     fetchDAS.setText(MessageManager.getString("label.fetch_das_features"));
     fetchDAS.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         fetchDAS_actionPerformed(e);
@@ -1154,6 +1180,7 @@ public class FeatureSettings extends JPanel implements
     saveDAS.setText(MessageManager.getString("action.save_as_default"));
     saveDAS.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         saveDAS_actionPerformed(e);
@@ -1165,6 +1192,7 @@ public class FeatureSettings extends JPanel implements
     cancelDAS.setText(MessageManager.getString("action.cancel_fetch"));
     cancelDAS.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         cancelDAS_actionPerformed(e);
@@ -1304,6 +1332,7 @@ public class FeatureSettings extends JPanel implements
       Runnable fetcher = new Runnable()
       {
 
+        @Override
         public void run()
         {
           doDasFeatureFetch(dassources, true, false);
@@ -1385,6 +1414,7 @@ public class FeatureSettings extends JPanel implements
       this.data = data;
     }
 
+    @Override
     public int getColumnCount()
     {
       return columnNames.length;
@@ -1395,31 +1425,37 @@ public class FeatureSettings extends JPanel implements
       return data[row];
     }
 
+    @Override
     public int getRowCount()
     {
       return data.length;
     }
 
+    @Override
     public String getColumnName(int col)
     {
       return columnNames[col];
     }
 
+    @Override
     public Object getValueAt(int row, int col)
     {
       return data[row][col];
     }
 
+    @Override
     public Class getColumnClass(int c)
     {
       return getValueAt(0, c).getClass();
     }
 
+    @Override
     public boolean isCellEditable(int row, int col)
     {
       return col == 0 ? false : true;
     }
 
+    @Override
     public void setValueAt(Object value, int row, int col)
     {
       data[row][col] = value;
@@ -1444,6 +1480,7 @@ public class FeatureSettings extends JPanel implements
       setVerticalTextPosition(SwingConstants.CENTER);
     }
 
+    @Override
     public Component getTableCellRendererComponent(JTable table,
             Object color, boolean isSelected, boolean hasFocus, int row,
             int column)
@@ -1609,16 +1646,19 @@ class FeatureIcon implements Icon
     }
   }
 
+  @Override
   public int getIconWidth()
   {
     return width;
   }
 
+  @Override
   public int getIconHeight()
   {
     return height;
   }
 
+  @Override
   public void paintIcon(Component c, Graphics g, int x, int y)
   {
 
@@ -1699,6 +1739,7 @@ class ColorEditor extends AbstractCellEditor implements TableCellEditor,
   /**
    * Handles events from the editor button and from the dialog's OK button.
    */
+  @Override
   public void actionPerformed(ActionEvent e)
   {
 
@@ -1744,6 +1785,7 @@ class ColorEditor extends AbstractCellEditor implements TableCellEditor,
   }
 
   // Implement the one CellEditor method that AbstractCellEditor doesn't.
+  @Override
   public Object getCellEditorValue()
   {
     if (currentColor == null)
@@ -1754,6 +1796,7 @@ class ColorEditor extends AbstractCellEditor implements TableCellEditor,
   }
 
   // Implement the one method defined by TableCellEditor.
+  @Override
   public Component getTableCellEditorComponent(JTable table, Object value,
           boolean isSelected, int row, int column)
   {

diff --git a/src/jalview/renderer/seqfeatures/FeatureRenderer.java b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
index 26bc895..2276913 100644 (file)
--- a/src/jalview/renderer/seqfeatures/FeatureRenderer.java
+++ b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
@@ -22,6 +22,7 @@ package jalview.renderer.seqfeatures;
 
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
+import jalview.viewmodel.seqfeatures.FeatureRendererModel;
 
 import java.awt.AlphaComposite;
 import java.awt.Color;
@@ -30,8 +31,7 @@ import java.awt.Graphics;
 import java.awt.Graphics2D;
 import java.awt.image.BufferedImage;
 
-public class FeatureRenderer extends
-        jalview.viewmodel.seqfeatures.FeatureRendererModel
+public class FeatureRenderer extends FeatureRendererModel
 {
 
   FontMetrics fm;
@@ -168,6 +168,7 @@ public class FeatureRenderer extends
 
   BufferedImage offscreenImage;
 
+  @Override
   public Color findFeatureColour(Color initialCol, SequenceI seq, int res)
   {
     return new Color(findFeatureColour(initialCol.getRGB(), seq, res));
@@ -415,6 +416,7 @@ public class FeatureRenderer extends
    * discover and display.
    * 
    */
+  @Override
   public void featuresAdded()
   {
     lastSeq = null;

diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
index 8db907c..e912720 100644 (file)
--- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
+++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
@@ -34,6 +34,7 @@ import java.beans.PropertyChangeListener;
 import java.beans.PropertyChangeSupport;
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.HashMap;
 import java.util.Hashtable;
 import java.util.Iterator;
 import java.util.List;
@@ -56,6 +57,9 @@ public abstract class FeatureRendererModel implements
 
   protected Object currentColour;
 
+  /*
+   * ordering of rendering, where last means on top
+   */
   protected String[] renderOrder;
 
   protected PropertyChangeSupport changeSupport = new PropertyChangeSupport(
@@ -63,6 +67,7 @@ public abstract class FeatureRendererModel implements
 
   protected AlignmentViewport av;
 
+  @Override
   public AlignViewportI getViewport()
   {
     return av;
@@ -537,6 +542,7 @@ public abstract class FeatureRendererModel implements
    * @param featureType
    * @return java.awt.Color or GraduatedColor
    */
+  @Override
   public Object getFeatureStyle(String featureType)
   {
     Object fc = featureColours.get(featureType);
@@ -617,6 +623,7 @@ public abstract class FeatureRendererModel implements
     return av.getFeaturesDisplayed().isVisible(type);
   }
 
+  @Override
   public void setColour(String featureType, Object col)
   {
     // overwrite
@@ -691,21 +698,32 @@ public abstract class FeatureRendererModel implements
    * 
    * @param data
    *          { String(Type), Colour(Type), Boolean(Displayed) }
+   * @return true if any visible features have been reordered, else false
    */
-  public void setFeaturePriority(Object[][] data)
+  public boolean setFeaturePriority(Object[][] data)
   {
-    setFeaturePriority(data, true);
+    return setFeaturePriority(data, true);
   }
 
   /**
+   * Sets the priority order for features
    * 
    * @param data
    *          { String(Type), Colour(Type), Boolean(Displayed) }
    * @param visibleNew
    *          when true current featureDisplay list will be cleared
+   * @return true if any visible features have been reordered or recoloured,
+   *         else false (i.e. no need to repaint)
    */
-  public void setFeaturePriority(Object[][] data, boolean visibleNew)
+  public boolean setFeaturePriority(Object[][] data, boolean visibleNew)
   {
+    /*
+     * note visible feature ordering and colours before update
+     */
+    List<String> visibleFeatures = getDisplayedFeatureTypes();
+    Map<String, Object> visibleColours = new HashMap<String, Object>(
+            getFeatureColours());
+
     FeaturesDisplayedI av_featuresdisplayed = null;
     if (visibleNew)
     {
@@ -724,10 +742,10 @@ public abstract class FeatureRendererModel implements
     }
     if (data == null)
     {
-      return;
+      return false;
     }
     // The feature table will display high priority
-    // features at the top, but theses are the ones
+    // features at the top, but these are the ones
     // we need to render last, so invert the data
     renderOrder = new String[data.length];
 
@@ -747,6 +765,30 @@ public abstract class FeatureRendererModel implements
       }
     }
 
+    /*
+     * get the new visible ordering and return true if it has changed
+     * order or any colour has changed
+     */
+    List<String> reorderedVisibleFeatures = getDisplayedFeatureTypes();
+    if (!visibleFeatures.equals(reorderedVisibleFeatures))
+    {
+      /*
+       * the list of ordered visible features has changed
+       */
+      return true;
+    }
+
+    /*
+     * return true if any feature colour has changed
+     */
+    for (String feature : visibleFeatures)
+    {
+      if (visibleColours.get(feature) != getFeatureStyle(feature))
+      {
+        return true;
+      }
+    }
+    return false;
   }
 
   /**
@@ -902,39 +944,39 @@ public abstract class FeatureRendererModel implements
     return av.getFeaturesDisplayed();
   }
 
+  /**
+   * Returns a (possibly empty) list of visible feature types, in render order
+   * (last is on top)
+   */
   @Override
-  public String[] getDisplayedFeatureTypes()
+  public List<String> getDisplayedFeatureTypes()
   {
-    String[] typ = null;
-    typ = getRenderOrder().toArray(new String[0]);
+    List<String> typ = getRenderOrder();
+    List<String> displayed = new ArrayList<String>();
     FeaturesDisplayedI feature_disp = av.getFeaturesDisplayed();
     if (feature_disp != null)
     {
       synchronized (feature_disp)
       {
-        for (int i = 0; i < typ.length; i++)
+        for (String type : typ)
         {
-          if (!feature_disp.isVisible(typ[i]))
+          if (feature_disp.isVisible(type))
           {
-            typ[i] = null;
+            displayed.add(type);
           }
         }
       }
     }
-    return typ;
+    return displayed;
   }
 
   @Override
-  public String[] getDisplayedFeatureGroups()
+  public List<String> getDisplayedFeatureGroups()
   {
-    String[] gps = null;
-    ArrayList<String> _gps = new ArrayList<String>();
-    Iterator en = getFeatureGroups().iterator();
-    int g = 0;
+    List<String> _gps = new ArrayList<String>();
     boolean valid = false;
-    while (en.hasNext())
+    for (String gp : getFeatureGroups())
     {
-      String gp = (String) en.next();
       if (checkGroupVisibility(gp, false))
       {
         valid = true;
@@ -946,11 +988,11 @@ public abstract class FeatureRendererModel implements
       }
       else
       {
-        gps = new String[_gps.size()];
-        _gps.toArray(gps);
+        // gps = new String[_gps.size()];
+        // _gps.toArray(gps);
       }
     }
-    return gps;
+    return _gps;
   }
 
 }

diff --git a/test/jalview/analysis/scoremodels/FeatureScoreModelTest.java b/test/jalview/analysis/scoremodels/FeatureScoreModelTest.java
index a70fac2..2dc2ac3 100644 (file)
--- a/test/jalview/analysis/scoremodels/FeatureScoreModelTest.java
+++ b/test/jalview/analysis/scoremodels/FeatureScoreModelTest.java
@@ -73,7 +73,7 @@ public class FeatureScoreModelTest
     alf.getFeatureRenderer().setVisible("sf3");
     alf.getFeatureRenderer().findAllFeatures(true);
     AssertJUnit.assertEquals("Number of feature types", 3, alf
-            .getFeatureRenderer().getDisplayedFeatureTypes().length);
+            .getFeatureRenderer().getDisplayedFeatureTypes().size());
     AssertJUnit.assertTrue(alf.getCurrentView().areFeaturesDisplayed());
     FeatureScoreModel fsm = new FeatureScoreModel();
     AssertJUnit.assertTrue(fsm.configureFromAlignmentView(alf